10-121488005-T-A

Position:

• chr10-121488005-T-A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_000141.5(FGFR2):​c.1972A>T​(p.Lys658*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FGFR2 NM_000141.5 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.98

Genes affected

FGFR2 (HGNC:3689): (fibroblast growth factor receptor 2) The protein encoded by this gene is a member of the fibroblast growth factor receptor family, where amino acid sequence is highly conserved between members and throughout evolution. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein consists of an extracellular region, composed of three immunoglobulin-like domains, a single hydrophobic membrane-spanning segment and a cytoplasmic tyrosine kinase domain. The extracellular portion of the protein interacts with fibroblast growth factors, setting in motion a cascade of downstream signals, ultimately influencing mitogenesis and differentiation. This particular family member is a high-affinity receptor for acidic, basic and/or keratinocyte growth factor, depending on the isoform. Mutations in this gene are associated with Crouzon syndrome, Pfeiffer syndrome, Craniosynostosis, Apert syndrome, Jackson-Weiss syndrome, Beare-Stevenson cutis gyrata syndrome, Saethre-Chotzen syndrome, and syndromic craniosynostosis. Multiple alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jan 2009]

FGFR2 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FGFR2	NM_000141.5	c.1972A>T	p.Lys658*	stop_gained	14/18	ENST00000358487.10	NP_000132.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FGFR2	ENST00000358487.10	c.1972A>T	p.Lys658*	stop_gained	14/18	1	NM_000141.5	ENSP00000351276.6
FGFR2	ENST00000457416.7	c.1975A>T	p.Lys659*	stop_gained	14/18	1		ENSP00000410294.2
FGFR2	ENST00000369056.5	c.1975A>T	p.Lys659*	stop_gained	13/17	1		ENSP00000358052.1
FGFR2	ENST00000369058.7	c.1975A>T	p.Lys659*	stop_gained	14/17	1		ENSP00000358054.3
FGFR2	ENST00000613048.4	c.1705A>T	p.Lys569*	stop_gained	13/17	5		ENSP00000484154.1
FGFR2	ENST00000369061.8	c.1636A>T	p.Lys546*	stop_gained	11/15	1		ENSP00000358057.4
FGFR2	ENST00000369059.5	c.1630A>T	p.Lys544*	stop_gained	12/16	5		ENSP00000358055.1
FGFR2	ENST00000360144.7	c.1708A>T	p.Lys570*	stop_gained	13/17	2		ENSP00000353262.3
FGFR2	ENST00000478859.5	c.1288A>T	p.Lys430*	stop_gained	13/17	1		ENSP00000474011.1
FGFR2	ENST00000429361.5	c.748A>T	p.Lys250*	stop_gained	6/9	5		ENSP00000404219.1
FGFR2	ENST00000604236.5	n.*1019A>T		non_coding_transcript_exon_variant	13/17	1		ENSP00000474109.1
FGFR2	ENST00000604236.5	n.*1019A>T		3_prime_UTR_variant	13/17	1		ENSP00000474109.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.62	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	48
DANN	Uncertain	1.0
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.79
FATHMM_MKL	Pathogenic	0.98	D
Vest4		0.94
GERP RS		5.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-123247519;